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If you use plots from MultiQC in a publication or presentation, please cite:

MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

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About MultiQC

This report was generated using MultiQC, version 1.0.dev0

You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

MultiQC is published in Bioinformatics:

MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

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Report generated on 2018-01-25, 06:01 based on data in: /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HF7VNBGX5/merged

General Statistics

Showing ⁴⁵/₄₅ rows and ³/₅ columns.

Sample Name	% Dups	% GC	Length	% Failed	M Seqs
HF7VNBGX5_n01_ko015_1	41.3%	45%	75 bp	17%	10.0
HF7VNBGX5_n01_ko015_2	40.4%	44%	75 bp	17%	10.7
HF7VNBGX5_n01_ko030_1	39.6%	46%	75 bp	17%	6.6
HF7VNBGX5_n01_ko030_2	41.8%	45%	75 bp	17%	10.7
HF7VNBGX5_n01_ko1015_1	41.2%	44%	75 bp	17%	10.3
HF7VNBGX5_n01_ko1015_2	41.6%	45%	75 bp	17%	11.4
HF7VNBGX5_n01_ko1030_1	42.2%	45%	75 bp	17%	10.4
HF7VNBGX5_n01_ko1030_2	35.1%	45%	75 bp	17%	5.3
HF7VNBGX5_n01_ko115_1	41.0%	44%	75 bp	17%	10.3
HF7VNBGX5_n01_ko115_2	40.5%	44%	75 bp	17%	10.3
HF7VNBGX5_n01_ko130_1	43.3%	45%	75 bp	17%	11.0
HF7VNBGX5_n01_ko130_2	38.3%	45%	75 bp	17%	8.3
HF7VNBGX5_n01_ko6015_1	42.0%	45%	75 bp	17%	11.0
HF7VNBGX5_n01_ko6015_2	40.5%	45%	75 bp	17%	9.5
HF7VNBGX5_n01_ko6030_1	42.8%	44%	75 bp	17%	11.0
HF7VNBGX5_n01_ko6030_2	41.7%	44%	75 bp	17%	9.5
HF7VNBGX5_n01_ox015_1	42.2%	45%	75 bp	17%	11.1
HF7VNBGX5_n01_ox015_2	41.9%	45%	75 bp	17%	9.8
HF7VNBGX5_n01_ox030_1	39.2%	45%	75 bp	17%	8.7
HF7VNBGX5_n01_ox030_2	37.1%	45%	75 bp	17%	7.3
HF7VNBGX5_n01_ox1015_1	41.0%	45%	75 bp	17%	9.6
HF7VNBGX5_n01_ox1015_2	44.4%	45%	75 bp	17%	12.4
HF7VNBGX5_n01_ox1030_1	41.7%	45%	75 bp	17%	9.6
HF7VNBGX5_n01_ox1030_2	39.3%	45%	75 bp	17%	8.2
HF7VNBGX5_n01_ox115_1	44.9%	45%	75 bp	17%	12.9
HF7VNBGX5_n01_ox115_2	43.2%	45%	75 bp	17%	11.9
HF7VNBGX5_n01_ox130_1	40.2%	45%	75 bp	17%	8.3
HF7VNBGX5_n01_ox130_2	39.1%	45%	75 bp	17%	8.7
HF7VNBGX5_n01_ox6015_1	41.1%	45%	75 bp	17%	9.6
HF7VNBGX5_n01_ox6015_2	39.1%	45%	75 bp	17%	8.1
HF7VNBGX5_n01_ox6030_1	39.7%	45%	75 bp	17%	8.4
HF7VNBGX5_n01_ox6030_2	43.4%	45%	75 bp	17%	10.5
HF7VNBGX5_n01_wt015_1	56.0%	44%	75 bp	33%	10.8
HF7VNBGX5_n01_wt015_2	46.6%	45%	75 bp	17%	14.7
HF7VNBGX5_n01_wt030_1	38.3%	45%	75 bp	17%	8.5
HF7VNBGX5_n01_wt030_2	41.7%	44%	75 bp	17%	9.9
HF7VNBGX5_n01_wt060_1	40.5%	45%	75 bp	17%	9.6
HF7VNBGX5_n01_wt1015_1	43.5%	45%	75 bp	17%	8.7
HF7VNBGX5_n01_wt1015_2	43.9%	45%	75 bp	17%	9.5
HF7VNBGX5_n01_wt1030_1	45.8%	45%	75 bp	17%	12.1
HF7VNBGX5_n01_wt1030_2	40.2%	45%	75 bp	17%	9.2
HF7VNBGX5_n01_wt115_1	40.8%	44%	75 bp	17%	8.8
HF7VNBGX5_n01_wt115_2	40.1%	45%	75 bp	17%	8.6
HF7VNBGX5_n01_wt130_1	43.0%	44%	75 bp	17%	11.9
HF7VNBGX5_n01_wt130_2	45.7%	44%	75 bp	17%	13.3

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

Sort	Group	Column	Description	ID	Scale
\|\|	FastQC	% Dups	% Duplicate Reads	`percent_duplicates`	None
\|\|	FastQC	% GC	Average % GC Content	`percent_gc`	None
\|\|	FastQC	Length	Average Sequence Length (bp)	`avg_sequence_length`	None
\|\|	FastQC	% Failed	Percentage of modules failed in FastQC report (includes those not plotted here)	`percent_fails`	None
\|\|	FastQC	M Seqs	Total Sequences (millions)	`total_sequences`	read_count

Run Statistics

Showing ¹/₁ rows and ⁴/₄ columns.

Number of Lanes	Total # of Single-End Reads	Total # PF Reads	Undetermined	% PhiX Aligned
4.0	499632478	464142493	3.6	1.2

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

Sort	Column	Description	ID	Scale
\|\|	Total # of Single-End Reads	Total # of Single-End Reads	`Total # of Single-End Reads`	None
\|\|	Total # PF Reads	Total # PF Reads	`Total # PF Reads`	None
\|\|	Undetermined	Undetermined	`Undetermined`	None
\|\|	% PhiX Aligned	% PhiX Aligned	`% PhiX Aligned`	None

Demultiplexing Report

Demultiplexing Report
Total Read Count: Total number of PF (Passing Filter) reads in this library.
Portion: The proportion of reads that represent the individual library in the entire Library Pool.
Perfect: The percentage of reads in this library which have a barcode perfectly matching the barcode specified in TuboWeb. The remainder of reads have mismatches upto the max number of mismatches specified in TuboWeb (Allowed barcode mismatch option in your Library Pool).

Showing ⁴⁵/₄₅ rows and ³/₃ columns.

Library	Total Read Count	Portion (%)	Perfect (%)
ox6030_1	8436304	1.9	100.0
wt1015_1	8731686	2.0	100.0
ox130_2	8697868	1.9	100.0
ox1015_2	12420309	2.8	100.0
wt1030_1	12118512	2.7	100.0
wt015_2	14742642	3.3	100.0
ko1030_1	10357357	2.3	100.0
ox1030_2	8173229	1.8	100.0
ko115_1	10319993	2.3	100.0
ko1030_2	5344296	1.2	100.0
ko6030_1	10965283	2.5	100.0
ox115_2	11908190	2.7	100.0
wt1015_2	9468766	2.1	100.0
ox6030_2	10487653	2.3	100.0
ox6015_2	8136617	1.8	100.0
ko030_1	6643658	1.5	100.0
ox030_2	7316382	1.6	100.0
ko6030_2	9516320	2.1	100.0
wt1030_2	9230339	2.1	100.0
ox015_1	11149521	2.5	100.0
ox6015_1	9619151	2.2	100.0
wt130_2	13304404	3.0	100.0
ox1030_1	9598343	2.1	100.0
ko130_2	8284882	1.9	100.0
ko130_1	11011250	2.5	100.0
wt030_1	8507488	1.9	100.0
ox130_1	8277758	1.9	100.0
ox1015_1	9568485	2.1	100.0
ko015_2	10678991	2.4	100.0
wt115_1	8825145	2.0	100.0
wt015_1	10841964	2.4	100.0
wt030_2	9906663	2.2	100.0
ox115_1	12891727	2.9	100.0
ko015_1	9998326	2.2	100.0
ko1015_2	11369791	2.5	100.0
ko6015_1	10963271	2.5	100.0
ko6015_2	9516924	2.1	100.0
wt060_1	9628000	2.2	100.0
wt115_2	8636683	1.9	100.0
ko1015_1	10269301	2.3	100.0
wt130_1	11890271	2.7	100.0
ox030_1	8662323	1.9	100.0
ko115_2	10260117	2.3	100.0
ox015_2	9842091	2.2	100.0
ko030_2	10678281	2.4	100.0

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

Sort	Column	Description	ID	Scale
\|\|	Total Read Count	Total Read Count	`Total Read Count`	None
\|\|	Portion (%)	Portion (%)	`Portion (%)`	None
\|\|	Perfect (%)	Perfect (%)	`Perfect (%)`	None

FastQC

FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

Sequence Quality Histograms

The mean quality value across each base position in the read. See the FastQC help.

Per Sequence Quality Scores

The number of reads with average quality scores. Shows if a subset of reads has poor quality. See the FastQC help.

Per Base Sequence Content

The proportion of each base position for which each of the four normal DNA bases has been called. See the FastQC help.

Click a heatmap row to see a line plot for that dataset.

rollover for sample name

Position: -

%T: -

%C: -

%A: -

%G: -

Per Sequence GC Content

The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content. See the FastQC help.

Per Base N Content

The percentage of base calls at each position for which an N was called. See the FastQC help.

Sequence Length Distribution

All samples have sequences of a single length (75bp).

Sequence Duplication Levels

The relative level of duplication found for every sequence. See the FastQC help.

Overrepresented sequences

The total amount of overrepresented sequences found in each library. See the FastQC help for further information.

Adapter Content

The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. See the FastQC help. Only samples with ≥ 0.1% adapter contamination are shown.

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General Statistics

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Demultiplexing Report

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FastQC

Sequence Quality Histograms

Per Sequence Quality Scores

Per Base Sequence Content

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Per Sequence GC Content

Per Base N Content

Sequence Length Distribution

Sequence Duplication Levels

Overrepresented sequences

Adapter Content

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